sknano.core.atoms.KDTAtoms

class sknano.core.atoms.KDTAtoms(atoms=None, copylist=True, deepcopy=False)

An Atoms sub-class for KDTree analysis.

Sub-class of XAtoms class, and a container class for lists of KDTAtom instances.

Parameters:

atoms : {None, sequence, KDTAtoms}, optional

if not None, then a list of KDTAtom instance objects or an existing KDTAtoms instance object.

copylist : bool, optional

perform shallow copy of atoms list

deepcopy : bool, optional

perform deepcopy of atoms list

Attributes

CM	Center-of-Mass coordinates of Atoms.
M	Total mass of Atoms.
NNrc	Only return neighbors within this distance when querying the kd-tree.
Natoms	Number of atoms in Atoms.
Ntypes	Number of atomtypes.
atom_ids	Return array of XAtom IDs.
atom_tree	scipy.spatial.KDTree of
atomtypes	atomtypes dict.
bonds	Return list of bonds.
bounds	Bounds of Atoms.
centroid	Centroid of Atoms.
charges	Return array of XAtom charges.
coordination_numbers	Return array of KDTAtom coordination numbers.
coords	numpy.ndarray of Atoms \(x, y, z\) coordinates.
inertia_tensor	Return the inertia tensor.
kNN	Number of nearest neighbors to return when querying the kd-tree.
masses	Return list of Atom masses.
nearest_neighbors	Return array of nearest-neighbor atoms for each KDTAtom.
q	Return the total net charge of XAtoms.
symbols	Return list of Atom symbols.
velocities	Return array of XAtom velocities.
x	numpy.ndarray of Atoms \(x\) coordinates.
y	numpy.ndarray of Atoms \(y\) coordinates.
z	numpy.ndarray of Atoms \(z\) coordinates.

Methods

add_atomtype(atom)	Add atom type to atomtypes.
add_atomtypes([atoms])	Add atomtype for each atom in atoms to atomtypes dictionary.
append(item)
assign_unique_ids([starting_id])	Assign unique ID to each XAtom in XAtoms.
center_CM([axes])	Center atoms on CM coordinates.
clear()
clip_bounds(region[, center_before_clipping])	Remove atoms outside the given limits along given dimension.
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Return Atoms by XAtoms.atom_ids in atom_ids.
get_atom(atomID)	Get XAtom with Xatom.atomID == atomID.
get_atoms([asarray])	Return list of Atoms.
get_coords([asdict])	Return atom coords.
getatomattr(attr)	Get numpy.ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr(attr, from_attr, attrmap)	Set/update atom attribute from another atom attribute with dict.
pop([i])
query_atom_tree([k, eps, p, rc])	Query atom tree for nearest neighbors distances and indices.
query_ball_point(pts, r[, p, eps])	Find all Atoms within distance r of point(s) pts.
remove(item)
reverse()
rezero([epsilon])	Set really really small coordinates to zero.
rezero_coords([epsilon])	Alias for Atoms.rezero.
rezero_xyz([epsilon])	Alias for Atoms.rezero.
rotate([angle, rot_axis, anchor_point, ...])	Rotate Atom position vectors.
select(cmd)
select_within(volume)
sort([key, reverse])
translate(t[, fix_anchor_points])	Translate Atom position vectors by Vector t.
update_attrs()	Update each KDTAtoms attributes.
update_bonds()	Update KDTAtom.bonds list.
update_coordination_numbers()	Update KDTAtom.CN.
update_nearest_neighbors()	Update KDTAtom.NN.